LAMMPS (8 Feb 2023)
Processor partition = 4
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
variable ibead uloop 8 pad

units           real
neigh_modify    delay 2 every 1

atom_style      full
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic

pair_style      lj/charmm/coul/long 11 12
pair_modify     mix arithmetic
kspace_style    pppm 1e-4

read_data system.data
Reading data file ...
  orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  8674 atoms
  reading velocities ...
  8674 velocities
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  18 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  reading bonds ...
  5869 bonds
  reading angles ...
  3264 angles
  reading dihedrals ...
  708 dihedrals
  reading impropers ...
  38 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     9 = max # of 1-3 neighbors
    17 = max # of 1-4 neighbors
    21 = max # of special neighbors
  special bonds CPU = 0.004 seconds
  read_data CPU = 0.138 seconds
#read_restart    system_${ibead}.rest1
special_bonds   charmm

fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0

thermo          10
thermo_style    custom step temp pe etotal f_1[1] f_1[2] f_1[3]
thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
timestep        0.08

# restart         100 system_${ibead}.rest1 system_${ibead}.rest2

group prot id <= 256
256 atoms in group prot
# dump 1 prot dcd 100 prot_${ibead}.dcd

run             200
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
  G vector (1/distance) = 0.22071363
  grid = 20 20 20
  stencil order = 5
  estimated absolute RMS force accuracy = 0.024910591
  estimated relative force accuracy = 7.5017505e-05
  using double precision KISS FFT
  3d grid and FFT values/proc = 15625 8000
Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 2 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 7 7 7
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
WARNING: Inconsistent image flags (src/domain.cpp:815)
Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes
   Step          Temp          PotEng         TotEng        espring         T_ring         virial    
         0   306.20099     -26166.171     -18250.089      0              0             -676.31071    
        10   23.892095     -26119.899     -25502.227      4.2771563      382.22944     -813.96512    
        20   27.051103     -26287.602     -25588.262      15.607084      432.76775     -745.77933    
        30   27.042026     -26290.973     -25591.867      35.550734      432.62253     -326.69805    
        40   19.133546     -26173.654     -25679.002      70.11544       306.10144     -11.324153    
        50   19.302675     -25883.61      -25384.586      121.68648      308.8072       290.09295    
        60   20.704866     -25425.468     -24890.194      201.50535      331.23967      650.74045    
        70   18.95281      -24809.575     -24319.596      321.84847      303.21         967.87686    
        80   20.178541     -24115.258     -23593.591      491.86818      322.81943      1230.7506    
        90   18.755289     -23448.841     -22963.969      726.07287      300.05003      1426.7932    
       100   18.159265     -22868.418     -22398.954      1013.598       290.51475      1609.3405    
       110   17.922985     -22283.38      -21820.025      1355.5366      286.7347       1483.5981    
       120   17.617358     -21583.469     -21128.015      1747.6539      281.84524      1444.208     
       130   17.233206     -20748.165     -20302.643      2173.0115      275.6995       1597.8139    
       140   17.06066      -19726.034     -19284.972      2629.6918      272.9391       1704.3744    
       150   17.004216     -18648.306     -18208.703      3099.2098      272.0361       2025.6026    
       160   17.414218     -17588.638     -17138.435      3580.8838      278.59537      2747.2565    
       170   17.295959     -16669.449     -16222.304      4058.5589      276.70344      3432.2976    
       180   17.706054     -15991.367     -15533.62       4524.6837      283.26421      4008.5413    
       190   17.649786     -15623.329     -15167.037      4968.3076      282.36402      4251.4209    
       200   17.914982     -15484.434     -15021.286      5382.5961      286.60667      4187.5146    
Loop time of 35.3335 on 1 procs for 200 steps with 8674 atoms

Performance: 0.039 ns/day, 613.428 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s
98.1% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 27.644     | 27.644     | 27.644     |   0.0 | 78.24
Bond    | 0.1292     | 0.1292     | 0.1292     |   0.0 |  0.37
Kspace  | 2.4108     | 2.4108     | 2.4108     |   0.0 |  6.82
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.12913    | 0.12913    | 0.12913    |   0.0 |  0.37
Output  | 0.0021704  | 0.0021704  | 0.0021704  |   0.0 |  0.01
Modify  | 4.959      | 4.959      | 4.959      |   0.0 | 14.03
Other   |            | 0.05951    |            |       |  0.17

Nlocal:           8674 ave        8674 max        8674 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          27366 ave       27366 max       27366 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 4485849
Ave neighs/atom = 517.16036
Ave special neighs/atom = 2.2573207
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:35
